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Cao S, Kalin ML, Huang X. EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules. J Comput Chem 2023; 44:1536-1549. [PMID: 36856731 DOI: 10.1002/jcc.27088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/24/2022] [Accepted: 01/29/2023] [Indexed: 03/02/2023]
Abstract
Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET-based solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self-consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D-RISM calculations compared to AMBER-RISM software. EPISOL consists of both a user-friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force-field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL.
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Affiliation(s)
- Siqin Cao
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael L Kalin
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Cao S, Qiu Y, Unarta IC, Goonetilleke EC, Huang X. The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions around Negatively Charged Biomolecules. J Phys Chem B 2022; 126:8632-8645. [PMID: 36282904 DOI: 10.1021/acs.jpcb.2c04431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 3D reference interaction site model (3DRISM) provides an efficient grid-based solvation model to compute the structural and thermodynamic properties of biomolecules in aqueous solutions. However, it remains challenging for existing 3DRISM methods to correctly predict water distributions around negatively charged solute molecules. In this paper, we first show that this challenge is mainly due to the orientation of water molecules in the first solvation shell of the negatively charged solute molecules. To properly consider this orientational preference, position-dependent two-body intramolecular correlations of solvent need to be included in the 3DRISM theory, but direct evaluations of these position-dependent two-body intramolecular correlations remain numerically intractable. To address this challenge, we introduce the Ion-Dipole Correction (IDC) to the 3DRISM theory, in which we incorporate the orientation preference of water molecules via an additional solute-solvent interaction term (i.e., the ion-dipole interaction) while keeping the formulism of the 3DRISM equation unchanged. We prove that this newly introduced IDC term is equivalent to an effective direct correlation function which can effectively consider the orientation effect that arises from position dependent two-body correlations. We first quantitatively validate our 3DRISM-IDC theory combined with the PSE3 closure on Cl-, [ClO]- (a two-site anion), and [NO2]- (a three-site anion). For all three anions, we show that our 3DRISM-IDC theory significantly outperforms the 3DRISM theory in accurately predicting the solvation structures in comparison to MD simulations, including RDFs and 3D water distributions. Furthermore, we have also demonstrated that the 3DRISM-IDC can improve the accuracy of hydration free-energy calculation for Cl-. We further demonstrate that our 3DRISM-IDC theory yields significant improvements over the 3DRISM theory when applied to compute the solvation structures for various negatively charged solute molecules, including adenosine triphosphate (ATP), a short peptide containing 19 residues, a DNA hairpin containing 24 nucleotides, and a riboswitch RNA molecule with 77 nucleotides. We expect that our 3DRISM-IDC-PSE3 solvation model holds great promise to be widely applied to study solvation properties for nucleic acids and other biomolecules containing negatively charged functional groups.
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Affiliation(s)
- Siqin Cao
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Yunrui Qiu
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Ilona C Unarta
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Eshani C Goonetilleke
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Xuhui Huang
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
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Li Y, Gao Q, Xu X, Li P, Zhao S. Solvent-evolution-coupled single ion diffusion into charged nanopores. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Lu C, Tang W, Dou Z, Xie P, Xu X, Zhao S. A reaction density functional theory study of solvent effects on keto-enol tautomerism and isomerization in pyruvic acid. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yagi T, Sato H. Density functional theory for molecular liquids based on interaction site model and self-consistent integral equations for site–site pair correlation functions. J Chem Phys 2020; 153:164102. [DOI: 10.1063/5.0022568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tomoaki Yagi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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Cai C, Tang W, Qiao C, Jiang P, Lu C, Zhao S, Liu H. A reaction density functional theory study of the solvent effect in prototype SN2 reactions in aqueous solution. Phys Chem Chem Phys 2019; 21:24876-24883. [DOI: 10.1039/c9cp03888d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Reaction density functional theory (RxDFT), combining quantum DFT with classical DFT, has been employed to investigate the solvent effect and free energy profiles of SN2 reactions in aqueous solution.
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Affiliation(s)
- Cheng Cai
- State Key Laboratory of Chemical Engineering and School of Chemical Engineering, East China University of Science and Technology
- Shanghai
- China
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
| | - Weiqiang Tang
- State Key Laboratory of Chemical Engineering and School of Chemical Engineering, East China University of Science and Technology
- Shanghai
- China
| | - Chongzhi Qiao
- State Key Laboratory of Chemical Engineering and School of Chemical Engineering, East China University of Science and Technology
- Shanghai
- China
| | - Peng Jiang
- State Key Laboratory of Chemical Engineering and School of Chemical Engineering, East China University of Science and Technology
- Shanghai
- China
| | - Changjie Lu
- State Key Laboratory of Chemical Engineering and School of Chemical Engineering, East China University of Science and Technology
- Shanghai
- China
| | - Shuangliang Zhao
- State Key Laboratory of Chemical Engineering and School of Chemical Engineering, East China University of Science and Technology
- Shanghai
- China
| | - Honglai Liu
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai
- China
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Sheng S, Miller M, Wu J. Molecular Theory of Hydration at Different Temperatures. J Phys Chem B 2017; 121:6898-6908. [DOI: 10.1021/acs.jpcb.7b04264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shijie Sheng
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Michael Miller
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jianzhong Wu
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
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Affiliation(s)
- Shijie Sheng
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Department of Mathematics, University of California, Riverside, CA, USA
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Ratkova EL, Palmer DS, Fedorov MV. Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy. Chem Rev 2015; 115:6312-56. [PMID: 26073187 DOI: 10.1021/cr5000283] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ekaterina L Ratkova
- †G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia.,‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - David S Palmer
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,§Department of Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, United Kingdom
| | - Maxim V Fedorov
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,∥Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, John Anderson Building, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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Zhao S, Liu Y, Chen X, Lu Y, Liu H, Hu Y. Unified Framework of Multiscale Density Functional Theories and Its Recent Applications. MESOSCALE MODELING IN CHEMICAL ENGINEERING PART II 2015. [DOI: 10.1016/bs.ache.2015.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Chuev GN, Vyalov I, Georgi N. Extraction of site-site bridge functions and effective pair potentials from simulations of polar molecular liquids. J Comput Chem 2014; 35:1010-23. [DOI: 10.1002/jcc.23586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 02/08/2014] [Accepted: 02/13/2014] [Indexed: 01/13/2023]
Affiliation(s)
- Gennady N. Chuev
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science; Pushchino Moscow Region 142290 Russia
| | - Ivan Vyalov
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
| | - Nikolaj Georgi
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
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Zhao S, Liu Y, Liu H, Wu J. Site-site direct correlation functions for three popular molecular models of liquid water. J Chem Phys 2013; 139:064509. [DOI: 10.1063/1.4817784] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Liu Y, Wu J. Communication: Long-range angular correlations in liquid water. J Chem Phys 2013; 139:041103. [DOI: 10.1063/1.4817321] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Zhao S, Liu H, Ramirez R, Borgis D. Accurate evaluation of the angular-dependent direct correlation function of water. J Chem Phys 2013; 139:034503. [DOI: 10.1063/1.4813400] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Liu Y, Zhao S, Wu J. A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains. J Chem Theory Comput 2013; 9:1896-908. [DOI: 10.1021/ct3010936] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Liu
- Departments of Chemical and
Environmental Engineering and Mathematics, University of California,
Riverside, California 92521, United States
| | - Shuangliang Zhao
- State Key Laboratory of Chemical
Engineering, East China University of Science and Technology, Shanghai,
200238, P. R. China
| | - Jianzhong Wu
- Departments of Chemical and
Environmental Engineering and Mathematics, University of California,
Riverside, California 92521, United States
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Chuev GN, Vyalov I, Georgi N. Extraction of atom–atom bridge and direct correlation functions from molecular simulations: A test for ambient water. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.01.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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